def test_plot_alignment_basic(tmpdir, renderer, mixed_fwd_cov_evoked): """Test plotting of -trans.fif files and MEG sensor layouts.""" # generate fiducials file for testing tempdir = str(tmpdir) fiducials_path = op.join(tempdir, 'fiducials.fif') fid = [{ 'coord_frame': 5, 'ident': 1, 'kind': 1, 'r': [-0.08061612, -0.02908875, -0.04131077] }, { 'coord_frame': 5, 'ident': 2, 'kind': 1, 'r': [0.00146763, 0.08506715, -0.03483611] }, { 'coord_frame': 5, 'ident': 3, 'kind': 1, 'r': [0.08436285, -0.02850276, -0.04127743] }] write_dig(fiducials_path, fid, 5) evoked = read_evokeds(evoked_fname)[0] info = evoked.info sample_src = read_source_spaces(src_fname) pytest.raises(TypeError, plot_alignment, 'foo', trans_fname, subject='sample', subjects_dir=subjects_dir) pytest.raises(OSError, plot_alignment, info, trans_fname, subject='sample', subjects_dir=subjects_dir, src='foo') pytest.raises(ValueError, plot_alignment, info, trans_fname, subject='fsaverage', subjects_dir=subjects_dir, src=sample_src) sample_src.plot(subjects_dir=subjects_dir, head=True, skull=True, brain='white') # mixed source space mixed_src = mixed_fwd_cov_evoked[0]['src'] assert mixed_src.kind == 'mixed' plot_alignment(info, meg=['helmet', 'sensors'], dig=True, coord_frame='head', trans=Path(trans_fname), subject='sample', mri_fiducials=fiducials_path, subjects_dir=subjects_dir, src=mixed_src) renderer.backend._close_all() # no-head version renderer.backend._close_all() # trans required with pytest.raises(ValueError, match='transformation matrix is required'): plot_alignment(info, trans=None, src=src_fname) with pytest.raises(ValueError, match='transformation matrix is required'): plot_alignment(info, trans=None, mri_fiducials=True) with pytest.raises(ValueError, match='transformation matrix is required'): plot_alignment(info, trans=None, surfaces=['brain']) # all coord frames plot_alignment(info) # works: surfaces='auto' default for coord_frame in ('meg', 'head', 'mri'): fig = plot_alignment(info, meg=['helmet', 'sensors'], dig=True, coord_frame=coord_frame, trans=Path(trans_fname), subject='sample', mri_fiducials=fiducials_path, subjects_dir=subjects_dir, src=src_fname) renderer.backend._close_all() # EEG only with strange options evoked_eeg_ecog_seeg = evoked.copy().pick_types(meg=False, eeg=True) evoked_eeg_ecog_seeg.info['projs'] = [] # "remove" avg proj evoked_eeg_ecog_seeg.set_channel_types({ 'EEG 001': 'ecog', 'EEG 002': 'seeg' }) with catch_logging() as log: plot_alignment(evoked_eeg_ecog_seeg.info, subject='sample', trans=trans_fname, subjects_dir=subjects_dir, surfaces=['white', 'outer_skin', 'outer_skull'], meg=['helmet', 'sensors'], eeg=['original', 'projected'], ecog=True, seeg=True, verbose=True) log = log.getvalue() assert 'ecog: 1' in log assert 'seeg: 1' in log renderer.backend._close_all() sphere = make_sphere_model(info=info, r0='auto', head_radius='auto') bem_sol = read_bem_solution( op.join(subjects_dir, 'sample', 'bem', 'sample-1280-1280-1280-bem-sol.fif')) bem_surfs = read_bem_surfaces( op.join(subjects_dir, 'sample', 'bem', 'sample-1280-1280-1280-bem.fif')) sample_src[0]['coord_frame'] = 4 # hack for coverage plot_alignment( info, trans_fname, subject='sample', eeg='projected', meg='helmet', bem=sphere, dig=True, surfaces=['brain', 'inner_skull', 'outer_skull', 'outer_skin']) plot_alignment(info, subject='sample', meg='helmet', subjects_dir=subjects_dir, eeg='projected', bem=sphere, surfaces=['head', 'brain'], src=sample_src) # no trans okay, no mri surfaces plot_alignment(info, bem=sphere, surfaces=['brain']) with pytest.raises(ValueError, match='A head surface is required'): plot_alignment(info, trans=trans_fname, subject='sample', subjects_dir=subjects_dir, eeg='projected', surfaces=[]) with pytest.raises(RuntimeError, match='No brain surface found'): plot_alignment(info, trans=trans_fname, subject='foo', subjects_dir=subjects_dir, surfaces=['brain']) assert all(surf['coord_frame'] == FIFF.FIFFV_COORD_MRI for surf in bem_sol['surfs']) plot_alignment(info, trans_fname, subject='sample', meg=[], subjects_dir=subjects_dir, bem=bem_sol, eeg=True, surfaces=['head', 'inflated', 'outer_skull', 'inner_skull']) assert all(surf['coord_frame'] == FIFF.FIFFV_COORD_MRI for surf in bem_sol['surfs']) plot_alignment(info, trans_fname, subject='sample', meg=True, subjects_dir=subjects_dir, surfaces=['head', 'inner_skull'], bem=bem_surfs) # single-layer BEM can still plot head surface assert bem_surfs[-1]['id'] == FIFF.FIFFV_BEM_SURF_ID_BRAIN bem_sol_homog = read_bem_solution( op.join(subjects_dir, 'sample', 'bem', 'sample-1280-bem-sol.fif')) for use_bem in (bem_surfs[-1:], bem_sol_homog): with catch_logging() as log: plot_alignment(info, trans_fname, subject='sample', meg=True, subjects_dir=subjects_dir, surfaces=['head', 'inner_skull'], bem=use_bem, verbose=True) log = log.getvalue() assert 'not find the surface for head in the provided BEM model' in log # sphere model sphere = make_sphere_model('auto', 'auto', info) src = setup_volume_source_space(sphere=sphere) plot_alignment( info, trans=Transform('head', 'mri'), eeg='projected', meg='helmet', bem=sphere, src=src, dig=True, surfaces=['brain', 'inner_skull', 'outer_skull', 'outer_skin']) sphere = make_sphere_model('auto', None, info) # one layer # if you ask for a brain surface with a 1-layer sphere model it's an error with pytest.raises(RuntimeError, match='Sphere model does not have'): fig = plot_alignment(trans=trans_fname, subject='sample', subjects_dir=subjects_dir, surfaces=['brain'], bem=sphere) # but you can ask for a specific brain surface, and # no info is permitted fig = plot_alignment(trans=trans_fname, subject='sample', meg=False, coord_frame='mri', subjects_dir=subjects_dir, surfaces=['white'], bem=sphere, show_axes=True) renderer.backend._close_all() if renderer._get_3d_backend() == 'mayavi': import mayavi # noqa: F401 analysis:ignore assert isinstance(fig, mayavi.core.scene.Scene) # 3D coil with no defined draw (ConvexHull) info_cube = pick_info(info, np.arange(6)) info['dig'] = None info_cube['chs'][0]['coil_type'] = 9999 info_cube['chs'][1]['coil_type'] = 9998 with pytest.raises(RuntimeError, match='coil definition not found'): plot_alignment(info_cube, meg='sensors', surfaces=()) coil_def_fname = op.join(tempdir, 'temp') with open(coil_def_fname, 'w') as fid: fid.write(coil_3d) # make sure our other OPMs can be plotted, too for ii, kind in enumerate( ('QUSPIN_ZFOPM_MAG', 'QUSPIN_ZFOPM_MAG2', 'FIELDLINE_OPM_MAG_GEN1', 'KERNEL_OPM_MAG_GEN1'), 2): info_cube['chs'][ii]['coil_type'] = getattr(FIFF, f'FIFFV_COIL_{kind}') with use_coil_def(coil_def_fname): with catch_logging() as log: plot_alignment(info_cube, meg='sensors', surfaces=(), dig=True, verbose='debug') log = log.getvalue() assert 'planar geometry' in log # one layer bem with skull surfaces: with pytest.raises(RuntimeError, match='Sphere model does not.*boundary'): plot_alignment(info=info, trans=trans_fname, subject='sample', subjects_dir=subjects_dir, surfaces=['brain', 'head', 'inner_skull'], bem=sphere) # wrong eeg value: with pytest.raises(ValueError, match='Invalid value for the .eeg'): plot_alignment(info=info, trans=trans_fname, subject='sample', subjects_dir=subjects_dir, eeg='foo') # wrong meg value: with pytest.raises(ValueError, match='Invalid value for the .meg'): plot_alignment(info=info, trans=trans_fname, subject='sample', subjects_dir=subjects_dir, meg='bar') # multiple brain surfaces: with pytest.raises(ValueError, match='Only one brain surface can be plot'): plot_alignment(info=info, trans=trans_fname, subject='sample', subjects_dir=subjects_dir, surfaces=['white', 'pial']) with pytest.raises(TypeError, match='surfaces.*must be'): plot_alignment(info=info, trans=trans_fname, subject='sample', subjects_dir=subjects_dir, surfaces=[1]) with pytest.raises(ValueError, match='Unknown surface type'): plot_alignment(info=info, trans=trans_fname, subject='sample', subjects_dir=subjects_dir, surfaces=['foo']) with pytest.raises(TypeError, match="must be an instance of "): plot_alignment(info=info, trans=trans_fname, subject='sample', subjects_dir=subjects_dir, surfaces=dict(brain='super clear')) with pytest.raises(ValueError, match="must be between 0 and 1"): plot_alignment(info=info, trans=trans_fname, subject='sample', subjects_dir=subjects_dir, surfaces=dict(brain=42)) fwd_fname = op.join(data_dir, 'MEG', 'sample', 'sample_audvis_trunc-meg-eeg-oct-4-fwd.fif') fwd = read_forward_solution(fwd_fname) plot_alignment(subject='sample', subjects_dir=subjects_dir, trans=trans_fname, fwd=fwd, surfaces='white', coord_frame='head') fwd = convert_forward_solution(fwd, force_fixed=True) plot_alignment(subject='sample', subjects_dir=subjects_dir, trans=trans_fname, fwd=fwd, surfaces='white', coord_frame='head') fwd['coord_frame'] = FIFF.FIFFV_COORD_MRI # check required to get to MRI with pytest.raises(ValueError, match='transformation matrix is required'): plot_alignment(info, trans=None, fwd=fwd) # surfaces as dict plot_alignment(subject='sample', coord_frame='head', trans=trans_fname, subjects_dir=subjects_dir, surfaces={ 'white': 0.4, 'outer_skull': 0.6, 'head': None })
def test_plot_alignment(tmpdir, renderer): """Test plotting of -trans.fif files and MEG sensor layouts.""" # generate fiducials file for testing tempdir = str(tmpdir) fiducials_path = op.join(tempdir, 'fiducials.fif') fid = [{ 'coord_frame': 5, 'ident': 1, 'kind': 1, 'r': [-0.08061612, -0.02908875, -0.04131077] }, { 'coord_frame': 5, 'ident': 2, 'kind': 1, 'r': [0.00146763, 0.08506715, -0.03483611] }, { 'coord_frame': 5, 'ident': 3, 'kind': 1, 'r': [0.08436285, -0.02850276, -0.04127743] }] write_dig(fiducials_path, fid, 5) renderer._close_all() evoked = read_evokeds(evoked_fname)[0] sample_src = read_source_spaces(src_fname) bti = read_raw_bti(pdf_fname, config_fname, hs_fname, convert=True, preload=False).info infos = dict( Neuromag=evoked.info, CTF=read_raw_ctf(ctf_fname).info, BTi=bti, KIT=read_raw_kit(sqd_fname).info, ) for system, info in infos.items(): meg = ['helmet', 'sensors'] if system == 'KIT': meg.append('ref') fig = plot_alignment(info, read_trans(trans_fname), subject='sample', subjects_dir=subjects_dir, meg=meg) rend = renderer._Renderer(fig=fig) rend.close() # KIT ref sensor coil def is defined renderer._close_all() info = infos['Neuromag'] pytest.raises(TypeError, plot_alignment, 'foo', trans_fname, subject='sample', subjects_dir=subjects_dir) pytest.raises(OSError, plot_alignment, info, trans_fname, subject='sample', subjects_dir=subjects_dir, src='foo') pytest.raises(ValueError, plot_alignment, info, trans_fname, subject='fsaverage', subjects_dir=subjects_dir, src=sample_src) sample_src.plot(subjects_dir=subjects_dir, head=True, skull=True, brain='white') renderer._close_all() # no-head version renderer._close_all() # all coord frames pytest.raises(ValueError, plot_alignment, info) plot_alignment(info, surfaces=[]) for coord_frame in ('meg', 'head', 'mri'): fig = plot_alignment(info, meg=['helmet', 'sensors'], dig=True, coord_frame=coord_frame, trans=Path(trans_fname), subject='sample', mri_fiducials=fiducials_path, subjects_dir=subjects_dir, src=src_fname) renderer._close_all() # EEG only with strange options evoked_eeg_ecog_seeg = evoked.copy().pick_types(meg=False, eeg=True) evoked_eeg_ecog_seeg.info['projs'] = [] # "remove" avg proj evoked_eeg_ecog_seeg.set_channel_types({ 'EEG 001': 'ecog', 'EEG 002': 'seeg' }) with pytest.warns(RuntimeWarning, match='Cannot plot MEG'): plot_alignment(evoked_eeg_ecog_seeg.info, subject='sample', trans=trans_fname, subjects_dir=subjects_dir, surfaces=['white', 'outer_skin', 'outer_skull'], meg=['helmet', 'sensors'], eeg=['original', 'projected'], ecog=True, seeg=True) renderer._close_all() sphere = make_sphere_model(info=evoked.info, r0='auto', head_radius='auto') bem_sol = read_bem_solution( op.join(subjects_dir, 'sample', 'bem', 'sample-1280-1280-1280-bem-sol.fif')) bem_surfs = read_bem_surfaces( op.join(subjects_dir, 'sample', 'bem', 'sample-1280-1280-1280-bem.fif')) sample_src[0]['coord_frame'] = 4 # hack for coverage plot_alignment( info, subject='sample', eeg='projected', meg='helmet', bem=sphere, dig=True, surfaces=['brain', 'inner_skull', 'outer_skull', 'outer_skin']) plot_alignment(info, trans_fname, subject='sample', meg='helmet', subjects_dir=subjects_dir, eeg='projected', bem=sphere, surfaces=['head', 'brain'], src=sample_src) assert all(surf['coord_frame'] == FIFF.FIFFV_COORD_MRI for surf in bem_sol['surfs']) plot_alignment(info, trans_fname, subject='sample', meg=[], subjects_dir=subjects_dir, bem=bem_sol, eeg=True, surfaces=['head', 'inflated', 'outer_skull', 'inner_skull']) assert all(surf['coord_frame'] == FIFF.FIFFV_COORD_MRI for surf in bem_sol['surfs']) plot_alignment(info, trans_fname, subject='sample', meg=True, subjects_dir=subjects_dir, surfaces=['head', 'inner_skull'], bem=bem_surfs) # single-layer BEM can still plot head surface assert bem_surfs[-1]['id'] == FIFF.FIFFV_BEM_SURF_ID_BRAIN bem_sol_homog = read_bem_solution( op.join(subjects_dir, 'sample', 'bem', 'sample-1280-bem-sol.fif')) for use_bem in (bem_surfs[-1:], bem_sol_homog): with catch_logging() as log: plot_alignment(info, trans_fname, subject='sample', meg=True, subjects_dir=subjects_dir, surfaces=['head', 'inner_skull'], bem=use_bem, verbose=True) log = log.getvalue() assert 'not find the surface for head in the provided BEM model' in log # sphere model sphere = make_sphere_model('auto', 'auto', evoked.info) src = setup_volume_source_space(sphere=sphere) plot_alignment( info, eeg='projected', meg='helmet', bem=sphere, src=src, dig=True, surfaces=['brain', 'inner_skull', 'outer_skull', 'outer_skin']) sphere = make_sphere_model('auto', None, evoked.info) # one layer # no info is permitted fig = plot_alignment(trans=trans_fname, subject='sample', meg=False, coord_frame='mri', subjects_dir=subjects_dir, surfaces=['brain'], bem=sphere, show_axes=True) renderer._close_all() if renderer.get_3d_backend() == 'mayavi': import mayavi # noqa: F401 analysis:ignore assert isinstance(fig, mayavi.core.scene.Scene) # 3D coil with no defined draw (ConvexHull) info_cube = pick_info(info, [0]) info['dig'] = None info_cube['chs'][0]['coil_type'] = 9999 with pytest.raises(RuntimeError, match='coil definition not found'): plot_alignment(info_cube, meg='sensors', surfaces=()) coil_def_fname = op.join(tempdir, 'temp') with open(coil_def_fname, 'w') as fid: fid.write(coil_3d) with use_coil_def(coil_def_fname): plot_alignment(info_cube, meg='sensors', surfaces=(), dig=True) # one layer bem with skull surfaces: with pytest.raises(ValueError, match='sphere conductor model must have'): plot_alignment(info=info, trans=trans_fname, subject='sample', subjects_dir=subjects_dir, surfaces=['brain', 'head', 'inner_skull'], bem=sphere) # wrong eeg value: with pytest.raises(ValueError, match='eeg must only contain'): plot_alignment(info=info, trans=trans_fname, subject='sample', subjects_dir=subjects_dir, eeg='foo') # wrong meg value: with pytest.raises(ValueError, match='meg must only contain'): plot_alignment(info=info, trans=trans_fname, subject='sample', subjects_dir=subjects_dir, meg='bar') # multiple brain surfaces: with pytest.raises(ValueError, match='Only one brain surface can be plot'): plot_alignment(info=info, trans=trans_fname, subject='sample', subjects_dir=subjects_dir, surfaces=['white', 'pial']) with pytest.raises(TypeError, match='all entries in surfaces must be'): plot_alignment(info=info, trans=trans_fname, subject='sample', subjects_dir=subjects_dir, surfaces=[1]) with pytest.raises(ValueError, match='Unknown surface type'): plot_alignment(info=info, trans=trans_fname, subject='sample', subjects_dir=subjects_dir, surfaces=['foo']) fwd_fname = op.join(data_dir, 'MEG', 'sample', 'sample_audvis_trunc-meg-eeg-oct-4-fwd.fif') fwd = read_forward_solution(fwd_fname) plot_alignment(subject='sample', subjects_dir=subjects_dir, trans=trans_fname, fwd=fwd, surfaces='white', coord_frame='head') fwd = convert_forward_solution(fwd, force_fixed=True) plot_alignment(subject='sample', subjects_dir=subjects_dir, trans=trans_fname, fwd=fwd, surfaces='white', coord_frame='head') # fNIRS info = read_raw_nirx(nirx_fname).info with catch_logging() as log: plot_alignment(info, subject='fsaverage', surfaces=(), verbose=True) log = log.getvalue() assert '26 fnirs locations' in log renderer._close_all()